diff --git a/src/base/plots.h b/include/cantera/base/plots.h
similarity index 100%
rename from src/base/plots.h
rename to include/cantera/base/plots.h
diff --git a/samples/cxx/bvp/stagnation.cpp b/samples/cxx/bvp/stagnation.cpp
index 2b32a6010..b92ff5138 100644
--- a/samples/cxx/bvp/stagnation.cpp
+++ b/samples/cxx/bvp/stagnation.cpp
@@ -8,9 +8,9 @@
 #include <time.h>
 
 #include "AxiStagnBVP.h"
-#include "ArrayViewer.h"
-#include "ctml.h"
-#include "MultiJac.h"
+#include "cantera/numerics/ArrayViewer.h"
+#include "cantera/base/ctml.h"
+#include "cantera/oneD/MultiJac.h"
 
 using namespace ctml;
 using namespace Cantera;
diff --git a/samples/cxx/kinetics1/example_utils.h b/samples/cxx/kinetics1/example_utils.h
index 7a577370a..694ae103f 100644
--- a/samples/cxx/kinetics1/example_utils.h
+++ b/samples/cxx/kinetics1/example_utils.h
@@ -1,8 +1,8 @@
 #ifndef CT_EXAMPLE_UTILS_H
 #define CT_EXAMPLE_UTILS_H
 
-#include <cantera/kernel/Array.h>
-#include <cantera/kernel/plots.h>
+#include <cantera/base/Array.h>
+#include <cantera/base/plots.h>
 
 // Save the temperature, density, pressure, and mole fractions at one
 // time
diff --git a/test/thermo/nasapoly.cpp b/test/thermo/nasapoly.cpp
index a036a7040..267acd2fa 100644
--- a/test/thermo/nasapoly.cpp
+++ b/test/thermo/nasapoly.cpp
@@ -1,5 +1,5 @@
 #include "gtest/gtest.h"
-#include "cantera/kernel/NasaPoly1.h"
+#include "cantera/thermo/NasaPoly1.h"
 
 namespace Cantera
 {
diff --git a/test_problems/ChemEquil_gri_matrix/gri_matrix.cpp b/test_problems/ChemEquil_gri_matrix/gri_matrix.cpp
index 5e5f984aa..40ea390cf 100644
--- a/test_problems/ChemEquil_gri_matrix/gri_matrix.cpp
+++ b/test_problems/ChemEquil_gri_matrix/gri_matrix.cpp
@@ -2,9 +2,9 @@
  *  Copyright 2002 California Institute of Technology
  */
 
-#include "Cantera.h"
-#include "IdealGasMix.h"
-#include "equilibrium.h"
+#include "cantera/Cantera.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equilibrium.h"
 
 using namespace std;
 using namespace Cantera;
diff --git a/test_problems/ChemEquil_gri_pairs/gri_pairs.cpp b/test_problems/ChemEquil_gri_pairs/gri_pairs.cpp
index 5c058d99a..896175718 100644
--- a/test_problems/ChemEquil_gri_pairs/gri_pairs.cpp
+++ b/test_problems/ChemEquil_gri_pairs/gri_pairs.cpp
@@ -3,14 +3,14 @@
  */
 
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "ThermoPhase.h"
-#include "IdealGasMix.h"
-#include "equil.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equil/equil.h"
 #else
-#include "Cantera.h"
-#include "IdealGasMix.h"
-#include "equilibrium.h"
+#include "cantera/Cantera.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equilibrium.h"
 #endif
 
 using namespace std;
diff --git a/test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp b/test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp
index 94f0fcb8b..744e3f6d4 100644
--- a/test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp
+++ b/test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp
@@ -1,12 +1,12 @@
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "ThermoPhase.h"
-#include "IdealGasMix.h"
-#include "equil.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equil/equil.h"
 #else
-#include "Cantera.h"
-#include "IdealGasMix.h"
-#include "equilibrium.h"
+#include "cantera/Cantera.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equilibrium.h"
 #endif
 
 
diff --git a/test_problems/CpJump/CpJump.cpp b/test_problems/CpJump/CpJump.cpp
index bfaa191bc..b929f0f31 100644
--- a/test_problems/CpJump/CpJump.cpp
+++ b/test_problems/CpJump/CpJump.cpp
@@ -3,14 +3,14 @@
  */
 
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "ThermoPhase.h"
-#include "IdealGasMix.h"
-#include "equil.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equil/equil.h"
 #else
-#include "Cantera.h"
-#include "IdealGasMix.h"
-#include "equilibrium.h"
+#include "cantera/Cantera.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equilibrium.h"
 #endif
 
 using namespace std;
diff --git a/test_problems/NASA9poly_test/NASA9poly_test.cpp b/test_problems/NASA9poly_test/NASA9poly_test.cpp
index a37a4b3ef..79c91e862 100644
--- a/test_problems/NASA9poly_test/NASA9poly_test.cpp
+++ b/test_problems/NASA9poly_test/NASA9poly_test.cpp
@@ -20,11 +20,11 @@ using namespace std;
 /*****************************************************************/
 /*****************************************************************/
 
-#include "Cantera.h"
-#include "transport.h"
-#include "IdealGasMix.h"
+#include "cantera/Cantera.h"
+#include "cantera/transport.h"
+#include "cantera/IdealGasMix.h"
 
-#include "kernel/TransportFactory.h"
+#include "cantera/transport/TransportFactory.h"
 
 using namespace Cantera;
 
diff --git a/test_problems/SConscript b/test_problems/SConscript
index 11eba570d..abc577513 100644
--- a/test_problems/SConscript
+++ b/test_problems/SConscript
@@ -2,6 +2,7 @@ from buildutils import *
 
 Import('env','buildTargets','installTargets')
 localenv = env.Clone()
+localenv.Append(CPPPATH=['#include', '#src'])
 
 os.environ['PYTHONPATH'] = pjoin(os.getcwd(), '..', 'Cantera', 'python')
 os.environ['CANTERA_DATA'] = pjoin(os.getcwd(), '..', 'data', 'inputs')
diff --git a/test_problems/VCSnonideal/NaCl_equil/nacl_equil.cpp b/test_problems/VCSnonideal/NaCl_equil/nacl_equil.cpp
index fe3ede9fb..ca4bce4ca 100644
--- a/test_problems/VCSnonideal/NaCl_equil/nacl_equil.cpp
+++ b/test_problems/VCSnonideal/NaCl_equil/nacl_equil.cpp
@@ -2,15 +2,15 @@
  *  Copyright 2002 California Institute of Technology
  */
 
-#include "Cantera.h"
-#include "equilibrium.h"
-#include "kernel/vcs_MultiPhaseEquil.h"
-#include "kernel/vcs_internal.h"
+#include "cantera/Cantera.h"
+#include "cantera/equilibrium.h"
+#include "cantera/equil/vcs_MultiPhaseEquil.h"
+#include "equil/vcs_internal.h"
 
-#include "kernel/ThermoFactory.h"
-#include "kernel/IdealGasPhase.h"
-#include "kernel/HMWSoln.h"
-#include "kernel/StoichSubstanceSSTP.h"
+#include "cantera/thermo/ThermoFactory.h"
+#include "cantera/thermo/IdealGasPhase.h"
+#include "cantera/thermo/HMWSoln.h"
+#include "cantera/thermo/StoichSubstanceSSTP.h"
 
 using namespace Cantera;
 using namespace std;
diff --git a/test_problems/VPsilane_test/silane_equil.cpp b/test_problems/VPsilane_test/silane_equil.cpp
index 798137b66..02e80cf96 100644
--- a/test_problems/VPsilane_test/silane_equil.cpp
+++ b/test_problems/VPsilane_test/silane_equil.cpp
@@ -2,12 +2,12 @@
  *  Copyright 2002 California Institute of Technology
  */
 
-#include "Cantera.h"
-#include "IdealGasMix.h"
-#include "equilibrium.h"
-#include "kernel/IdealSolnGasVPSS.h"
-#include "kernel/ThermoFactory.h"
-#include "kernel/PrintCtrl.h"
+#include "cantera/Cantera.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equilibrium.h"
+#include "cantera/thermo/IdealSolnGasVPSS.h"
+#include "cantera/thermo/ThermoFactory.h"
+#include "cantera/base/PrintCtrl.h"
 
 using namespace std;
 using namespace Cantera;
diff --git a/test_problems/cathermo/DH_graph_1/DH_graph_1.cpp b/test_problems/cathermo/DH_graph_1/DH_graph_1.cpp
index ee5c774fc..36ba2f905 100644
--- a/test_problems/cathermo/DH_graph_1/DH_graph_1.cpp
+++ b/test_problems/cathermo/DH_graph_1/DH_graph_1.cpp
@@ -3,13 +3,13 @@
  *  @file DH_graph_1
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
-#include "DebyeHuckel.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #else
-#include "Cantera.h"
-#include "kernel/logger.h"
-#include "kernel/DebyeHuckel.h"
+#include "cantera/Cantera.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #endif
 #include <cstdio>
 
diff --git a/test_problems/cathermo/DH_graph_NM/DH_graph_1.cpp b/test_problems/cathermo/DH_graph_NM/DH_graph_1.cpp
index fd34b6a37..9a84d4eb5 100644
--- a/test_problems/cathermo/DH_graph_NM/DH_graph_1.cpp
+++ b/test_problems/cathermo/DH_graph_NM/DH_graph_1.cpp
@@ -3,13 +3,13 @@
  *  @file DH_graph_1
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
-#include "DebyeHuckel.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #else
-#include "Cantera.h"
-#include "kernel/logger.h"
-#include "kernel/DebyeHuckel.h"
+#include "cantera/Cantera.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/DH_graph_Pitzer/DH_graph_1.cpp b/test_problems/cathermo/DH_graph_Pitzer/DH_graph_1.cpp
index fd34b6a37..9a84d4eb5 100644
--- a/test_problems/cathermo/DH_graph_Pitzer/DH_graph_1.cpp
+++ b/test_problems/cathermo/DH_graph_Pitzer/DH_graph_1.cpp
@@ -3,13 +3,13 @@
  *  @file DH_graph_1
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
-#include "DebyeHuckel.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #else
-#include "Cantera.h"
-#include "kernel/logger.h"
-#include "kernel/DebyeHuckel.h"
+#include "cantera/Cantera.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/DH_graph_acommon/DH_graph_1.cpp b/test_problems/cathermo/DH_graph_acommon/DH_graph_1.cpp
index fd34b6a37..9a84d4eb5 100644
--- a/test_problems/cathermo/DH_graph_acommon/DH_graph_1.cpp
+++ b/test_problems/cathermo/DH_graph_acommon/DH_graph_1.cpp
@@ -3,13 +3,13 @@
  *  @file DH_graph_1
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
-#include "DebyeHuckel.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #else
-#include "Cantera.h"
-#include "kernel/logger.h"
-#include "kernel/DebyeHuckel.h"
+#include "cantera/Cantera.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/DH_graph_bdotak/DH_graph_1.cpp b/test_problems/cathermo/DH_graph_bdotak/DH_graph_1.cpp
index fd34b6a37..9a84d4eb5 100644
--- a/test_problems/cathermo/DH_graph_bdotak/DH_graph_1.cpp
+++ b/test_problems/cathermo/DH_graph_bdotak/DH_graph_1.cpp
@@ -3,13 +3,13 @@
  *  @file DH_graph_1
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
-#include "DebyeHuckel.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #else
-#include "Cantera.h"
-#include "kernel/logger.h"
-#include "kernel/DebyeHuckel.h"
+#include "cantera/Cantera.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/DebyeHuckel.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp b/test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp
index 24ee17eb1..fc9cb67a6 100644
--- a/test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp
+++ b/test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp
@@ -3,18 +3,18 @@
  *  @file HMW_graph_1.cpp
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
 #include "TemperatureTable.h"
-#include "ThermoPhase.h"
-#include "HMWSoln.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/thermo/HMWSoln.h"
 #include "importCTML.h"
 #else
-#include "Cantera.h"
-#include "kernel/logger.h"
-#include "thermo.h"
+#include "cantera/Cantera.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo.h"
 #include "TemperatureTable.h"
-#include "kernel/HMWSoln.h"
+#include "cantera/thermo/HMWSoln.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/HMW_dupl_test/TemperatureTable.h b/test_problems/cathermo/HMW_dupl_test/TemperatureTable.h
index ec36b778d..3f072a212 100644
--- a/test_problems/cathermo/HMW_dupl_test/TemperatureTable.h
+++ b/test_problems/cathermo/HMW_dupl_test/TemperatureTable.h
@@ -7,7 +7,7 @@
 
 #ifndef TEMPERATURE_TABLE_H
 #define  TEMPERATURE_TABLE_H
-//#include "mdp_allo.h"
+//#include "cantera/base/mdp_allo.h"
 #include <vector>
 using std::vector;
 
diff --git a/test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp b/test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp
index 2a119b08c..8d3dc078c 100644
--- a/test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp
+++ b/test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp
@@ -3,18 +3,18 @@
  *  @file HMW_graph_1.cpp
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
 #include "TemperatureTable.h"
-#include "ThermoPhase.h"
-#include "HMWSoln.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/thermo/HMWSoln.h"
 #include "importCTML.h"
 #else
-#include "Cantera.h"
-#include "kernel/logger.h"
-#include "thermo.h"
+#include "cantera/Cantera.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo.h"
 #include "TemperatureTable.h"
-#include "kernel/HMWSoln.h"
+#include "cantera/thermo/HMWSoln.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/HMW_graph_CpvT/TemperatureTable.h b/test_problems/cathermo/HMW_graph_CpvT/TemperatureTable.h
index ec36b778d..3f072a212 100644
--- a/test_problems/cathermo/HMW_graph_CpvT/TemperatureTable.h
+++ b/test_problems/cathermo/HMW_graph_CpvT/TemperatureTable.h
@@ -7,7 +7,7 @@
 
 #ifndef TEMPERATURE_TABLE_H
 #define  TEMPERATURE_TABLE_H
-//#include "mdp_allo.h"
+//#include "cantera/base/mdp_allo.h"
 #include <vector>
 using std::vector;
 
diff --git a/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp b/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
index b1f4d3a9b..8c20aec91 100644
--- a/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
+++ b/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
@@ -2,10 +2,10 @@
  *
  *  @file HMW_graph_1.cpp
  */
-#include "Cantera.h"
+#include "cantera/Cantera.h"
 
-#include "kernel/logger.h"
-#include "kernel/HMWSoln.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/HMWSoln.h"
 
 #include <cstdio>
 
diff --git a/test_problems/cathermo/HMW_graph_GvI/TemperatureTable.h b/test_problems/cathermo/HMW_graph_GvI/TemperatureTable.h
index ec36b778d..3f072a212 100644
--- a/test_problems/cathermo/HMW_graph_GvI/TemperatureTable.h
+++ b/test_problems/cathermo/HMW_graph_GvI/TemperatureTable.h
@@ -7,7 +7,7 @@
 
 #ifndef TEMPERATURE_TABLE_H
 #define  TEMPERATURE_TABLE_H
-//#include "mdp_allo.h"
+//#include "cantera/base/mdp_allo.h"
 #include <vector>
 using std::vector;
 
diff --git a/test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp b/test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp
index b5d0eafcb..afd0eba5d 100644
--- a/test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp
+++ b/test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp
@@ -3,17 +3,17 @@
  *  @file HMW_graph_1.cpp
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
-#include "ThermoPhase.h"
-#include "HMWSoln.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/thermo/HMWSoln.h"
 #include "importCTML.h"
 #else
-#include "Cantera.h"
-#include "kernel/ThermoPhase.h"
-#include "kernel/logger.h"
-#include "thermo.h"
-#include "kernel/HMWSoln.h"
+#include "cantera/Cantera.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo.h"
+#include "cantera/thermo/HMWSoln.h"
 #endif
 
 #include "TemperatureTable.h"
diff --git a/test_problems/cathermo/HMW_graph_GvT/TemperatureTable.h b/test_problems/cathermo/HMW_graph_GvT/TemperatureTable.h
index ec36b778d..3f072a212 100644
--- a/test_problems/cathermo/HMW_graph_GvT/TemperatureTable.h
+++ b/test_problems/cathermo/HMW_graph_GvT/TemperatureTable.h
@@ -7,7 +7,7 @@
 
 #ifndef TEMPERATURE_TABLE_H
 #define  TEMPERATURE_TABLE_H
-//#include "mdp_allo.h"
+//#include "cantera/base/mdp_allo.h"
 #include <vector>
 using std::vector;
 
diff --git a/test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp b/test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp
index 687e8a61a..7cea978b3 100644
--- a/test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp
+++ b/test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp
@@ -2,9 +2,9 @@
  *
  *  @file HMW_graph_1.cpp
  */
-#include "Cantera.h"
-#include "thermo.h"
-#include "kernel/HMWSoln.h"
+#include "cantera/Cantera.h"
+#include "cantera/thermo.h"
+#include "cantera/thermo/HMWSoln.h"
 #include "TemperatureTable.h"
 
 #include <cstdio>
diff --git a/test_problems/cathermo/HMW_graph_HvT/TemperatureTable.h b/test_problems/cathermo/HMW_graph_HvT/TemperatureTable.h
index ec36b778d..3f072a212 100644
--- a/test_problems/cathermo/HMW_graph_HvT/TemperatureTable.h
+++ b/test_problems/cathermo/HMW_graph_HvT/TemperatureTable.h
@@ -7,7 +7,7 @@
 
 #ifndef TEMPERATURE_TABLE_H
 #define  TEMPERATURE_TABLE_H
-//#include "mdp_allo.h"
+//#include "cantera/base/mdp_allo.h"
 #include <vector>
 using std::vector;
 
diff --git a/test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp b/test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp
index 0d2301f09..cc43a7b92 100644
--- a/test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp
+++ b/test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp
@@ -2,20 +2,20 @@
  *  @file HMW_graph_VvT
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
 #include "TemperatureTable.h"
-#include "HMWSoln.h"
+#include "cantera/thermo/HMWSoln.h"
 #include "importCTML.h"
 #else
 //#include "vcsc.h"
-#include "Cantera.h"
+#include "cantera/Cantera.h"
 //#include "vcs_Cantera_input.h"
 //#include "vcs_Cantera_convert.h"
-#include "kernel/logger.h"
-#include "thermo.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo.h"
 #include "TemperatureTable.h"
-#include "kernel/HMWSoln.h"
+#include "cantera/thermo/HMWSoln.h"
 
 #endif
 
diff --git a/test_problems/cathermo/HMW_graph_VvT/TemperatureTable.h b/test_problems/cathermo/HMW_graph_VvT/TemperatureTable.h
index ec36b778d..3f072a212 100644
--- a/test_problems/cathermo/HMW_graph_VvT/TemperatureTable.h
+++ b/test_problems/cathermo/HMW_graph_VvT/TemperatureTable.h
@@ -7,7 +7,7 @@
 
 #ifndef TEMPERATURE_TABLE_H
 #define  TEMPERATURE_TABLE_H
-//#include "mdp_allo.h"
+//#include "cantera/base/mdp_allo.h"
 #include <vector>
 using std::vector;
 
diff --git a/test_problems/cathermo/HMW_test_1/HMW_test_1.cpp b/test_problems/cathermo/HMW_test_1/HMW_test_1.cpp
index 04b3fd88e..5ff24f443 100644
--- a/test_problems/cathermo/HMW_test_1/HMW_test_1.cpp
+++ b/test_problems/cathermo/HMW_test_1/HMW_test_1.cpp
@@ -1,5 +1,5 @@
-#include "Cantera.h"
-#include "kernel/HMWSoln.h"
+#include "cantera/Cantera.h"
+#include "cantera/thermo/HMWSoln.h"
 
 #include <cstdio>
 
diff --git a/test_problems/cathermo/HMW_test_3/HMW_test_3.cpp b/test_problems/cathermo/HMW_test_3/HMW_test_3.cpp
index 758e60258..6e1c144ec 100644
--- a/test_problems/cathermo/HMW_test_3/HMW_test_3.cpp
+++ b/test_problems/cathermo/HMW_test_3/HMW_test_3.cpp
@@ -1,9 +1,9 @@
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "HMWSoln.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/thermo/HMWSoln.h"
 #else
-#include "Cantera.h"
-#include "kernel/HMWSoln.h"
+#include "cantera/Cantera.h"
+#include "cantera/thermo/HMWSoln.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/VPissp/ISSPTester.cpp b/test_problems/cathermo/VPissp/ISSPTester.cpp
index c6a58cb43..7f5730009 100644
--- a/test_problems/cathermo/VPissp/ISSPTester.cpp
+++ b/test_problems/cathermo/VPissp/ISSPTester.cpp
@@ -20,9 +20,9 @@
 #include <vector>
 
 
-#include "Cantera.h"
-#include "kernel/IdealSolidSolnPhase.h"
-#include "kernel/IdealSolnGasVPSS.h"
+#include "cantera/Cantera.h"
+#include "cantera/thermo/IdealSolidSolnPhase.h"
+#include "cantera/thermo/IdealSolnGasVPSS.h"
 
 #include <cstdio>
 
diff --git a/test_problems/cathermo/ims/IMSTester.cpp b/test_problems/cathermo/ims/IMSTester.cpp
index c358c4971..61ef5f92d 100644
--- a/test_problems/cathermo/ims/IMSTester.cpp
+++ b/test_problems/cathermo/ims/IMSTester.cpp
@@ -19,11 +19,11 @@
 #include <vector>
 
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "IdealMolalSoln.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/thermo/IdealMolalSoln.h"
 #else
-#include "Cantera.h"
-#include "kernel/IdealMolalSoln.h"
+#include "cantera/Cantera.h"
+#include "cantera/thermo/IdealMolalSoln.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/issp/ISSPTester.cpp b/test_problems/cathermo/issp/ISSPTester.cpp
index 7df1de291..3a91eac90 100644
--- a/test_problems/cathermo/issp/ISSPTester.cpp
+++ b/test_problems/cathermo/issp/ISSPTester.cpp
@@ -20,11 +20,11 @@
 #include <vector>
 
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "IdealSolidSolnPhase.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/thermo/IdealSolidSolnPhase.h"
 #else
-#include "Cantera.h"
-#include "kernel/IdealSolidSolnPhase.h"
+#include "cantera/Cantera.h"
+#include "cantera/thermo/IdealSolidSolnPhase.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/stoichSubSSTP/TemperatureTable.h b/test_problems/cathermo/stoichSubSSTP/TemperatureTable.h
index ec36b778d..3f072a212 100644
--- a/test_problems/cathermo/stoichSubSSTP/TemperatureTable.h
+++ b/test_problems/cathermo/stoichSubSSTP/TemperatureTable.h
@@ -7,7 +7,7 @@
 
 #ifndef TEMPERATURE_TABLE_H
 #define  TEMPERATURE_TABLE_H
-//#include "mdp_allo.h"
+//#include "cantera/base/mdp_allo.h"
 #include <vector>
 using std::vector;
 
diff --git a/test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp b/test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp
index 8cd813751..70dbfb97c 100644
--- a/test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp
+++ b/test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp
@@ -3,15 +3,15 @@
  *  @file HMW_graph_1.cpp
  */
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
-#include "ThermoPhase.h"
-#include "StoichSubstanceSSTP.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/logger.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/thermo/StoichSubstanceSSTP.h"
 #include "importCTML.h"
 #else
-#include "Cantera.h"
-#include "thermo.h"
-#include "kernel/StoichSubstanceSSTP.h"
+#include "cantera/Cantera.h"
+#include "cantera/thermo.h"
+#include "cantera/thermo/StoichSubstanceSSTP.h"
 #endif
 
 #include "TemperatureTable.h"
diff --git a/test_problems/cathermo/testIAPWS/testIAPWSphi.cpp b/test_problems/cathermo/testIAPWS/testIAPWSphi.cpp
index f4b494304..52cdb5de6 100644
--- a/test_problems/cathermo/testIAPWS/testIAPWSphi.cpp
+++ b/test_problems/cathermo/testIAPWS/testIAPWSphi.cpp
@@ -1,4 +1,4 @@
-#include "kernel/WaterPropsIAPWSphi.h"
+#include "cantera/thermo/WaterPropsIAPWSphi.h"
 #include <new>
 
 #include <cstdio>
diff --git a/test_problems/cathermo/testIAPWSPres/testPress.cpp b/test_problems/cathermo/testIAPWSPres/testPress.cpp
index 5641ee012..a9f2ad171 100644
--- a/test_problems/cathermo/testIAPWSPres/testPress.cpp
+++ b/test_problems/cathermo/testIAPWSPres/testPress.cpp
@@ -1,5 +1,5 @@
 
-#include "kernel/WaterPropsIAPWS.h"
+#include "cantera/thermo/WaterPropsIAPWS.h"
 #include <new>
 
 #include <cstdio>
diff --git a/test_problems/cathermo/testIAPWSTripP/testTripleP.cpp b/test_problems/cathermo/testIAPWSTripP/testTripleP.cpp
index 352f26212..a4ccd2662 100644
--- a/test_problems/cathermo/testIAPWSTripP/testTripleP.cpp
+++ b/test_problems/cathermo/testIAPWSTripP/testTripleP.cpp
@@ -1,5 +1,5 @@
 
-#include "kernel/WaterPropsIAPWS.h"
+#include "cantera/thermo/WaterPropsIAPWS.h"
 #include <new>
 
 #include <cstdio>
diff --git a/test_problems/cathermo/testWaterPDSS/testWaterPDSS.cpp b/test_problems/cathermo/testWaterPDSS/testWaterPDSS.cpp
index 47aff525a..d4324ec57 100644
--- a/test_problems/cathermo/testWaterPDSS/testWaterPDSS.cpp
+++ b/test_problems/cathermo/testWaterPDSS/testWaterPDSS.cpp
@@ -1,11 +1,11 @@
-#include "kernel/ct_defs.h"
-#include "kernel/ctexceptions.h"
-#include "kernel/global.h"
-#include "kernel/xml.h"
-#include "kernel/ctml.h"
-#include "kernel/PDSS_Water.h"
-#include "kernel/ThermoPhase.h"
-#include "kernel/VPStandardStateTP.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/ctexceptions.h"
+#include "cantera/base/global.h"
+#include "cantera/base/xml.h"
+#include "cantera/base/ctml.h"
+#include "cantera/thermo/PDSS_Water.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/thermo/VPStandardStateTP.h"
 #include <new>
 
 #include <cstdio>
diff --git a/test_problems/cathermo/testWaterTP/testWaterSSTP.cpp b/test_problems/cathermo/testWaterTP/testWaterSSTP.cpp
index 59ceaefa8..c3e4768ce 100644
--- a/test_problems/cathermo/testWaterTP/testWaterSSTP.cpp
+++ b/test_problems/cathermo/testWaterTP/testWaterSSTP.cpp
@@ -1,6 +1,6 @@
-#include "Cantera.h"
-#include "thermo.h"
-#include "kernel/WaterSSTP.h"
+#include "cantera/Cantera.h"
+#include "cantera/thermo.h"
+#include "cantera/thermo/WaterSSTP.h"
 
 #include <cstdio>
 #include <cmath>
diff --git a/test_problems/cathermo/wtWater/wtWater.cpp b/test_problems/cathermo/wtWater/wtWater.cpp
index 5cb5a912c..cce890e84 100644
--- a/test_problems/cathermo/wtWater/wtWater.cpp
+++ b/test_problems/cathermo/wtWater/wtWater.cpp
@@ -1,14 +1,14 @@
 
-#include "kernel/ct_defs.h"
-#include "kernel/ctexceptions.h"
-#include "kernel/global.h"
-#include "kernel/xml.h"
-#include "kernel/ctml.h"
-#include "kernel/ThermoPhase.h"
-#include "kernel/VPStandardStateTP.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/ctexceptions.h"
+#include "cantera/base/global.h"
+#include "cantera/base/xml.h"
+#include "cantera/base/ctml.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/thermo/VPStandardStateTP.h"
 
-#include "kernel/WaterSSTP.h"
-#include "kernel/WaterTransport.h"
+#include "cantera/thermo/WaterSSTP.h"
+#include "cantera/transport/WaterTransport.h"
 #include <new>
 
 #include <cstdio>
diff --git a/test_problems/cxx_ex/example_utils.h b/test_problems/cxx_ex/example_utils.h
index 743947169..f6be1c753 100644
--- a/test_problems/cxx_ex/example_utils.h
+++ b/test_problems/cxx_ex/example_utils.h
@@ -1,8 +1,8 @@
 #ifndef CT_EXAMPLE_UTILS_H
 #define CT_EXAMPLE_UTILS_H
 
-#include <cantera/kernel/Array.h>
-#include <cantera/kernel/plots.h>
+#include <cantera/base/Array.h>
+#include <cantera/base/plots.h>
 
 // Save the temperature, density, pressure, and mole fractions at one
 // time
diff --git a/test_problems/diamondSurf/runDiamond.cpp b/test_problems/diamondSurf/runDiamond.cpp
index f889beb88..80be9819e 100644
--- a/test_problems/diamondSurf/runDiamond.cpp
+++ b/test_problems/diamondSurf/runDiamond.cpp
@@ -26,8 +26,8 @@ int iDebug_HKM = 0;
 /*****************************************************************/
 /*****************************************************************/
 
-#include "Cantera.h"
-#include "kinetics.h"
+#include "cantera/Cantera.h"
+#include "cantera/kinetics.h"
 
 
 using namespace Cantera;
diff --git a/test_problems/diamondSurf_dupl/runDiamondDupl.cpp b/test_problems/diamondSurf_dupl/runDiamondDupl.cpp
index 2d9210542..f734dd0ba 100644
--- a/test_problems/diamondSurf_dupl/runDiamondDupl.cpp
+++ b/test_problems/diamondSurf_dupl/runDiamondDupl.cpp
@@ -26,8 +26,8 @@ int iDebug_HKM = 0;
 /*****************************************************************/
 /*****************************************************************/
 
-#include "Cantera.h"
-#include "kinetics.h"
+#include "cantera/Cantera.h"
+#include "cantera/kinetics.h"
 
 
 using namespace Cantera;
diff --git a/test_problems/fracCoeff/fracCoeff.cpp b/test_problems/fracCoeff/fracCoeff.cpp
index 5f2d3313c..77499e2e5 100644
--- a/test_problems/fracCoeff/fracCoeff.cpp
+++ b/test_problems/fracCoeff/fracCoeff.cpp
@@ -28,15 +28,15 @@ int iDebug_HKM = 0;
 /*****************************************************************/
 
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "ctml.h"
-#include "GasKinetics.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/ctml.h"
+#include "cantera/kinetics/GasKinetics.h"
 #include "importCTML.h"
-#include "ThermoPhase.h"
-#include "InterfaceKinetics.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/kinetics/InterfaceKinetics.h"
 #else
-#include "Cantera.h"
-#include "kinetics.h"
+#include "cantera/Cantera.h"
+#include "cantera/kinetics.h"
 #endif
 
 using namespace Cantera;
diff --git a/test_problems/min_python/minDiamond/runDiamond.cpp b/test_problems/min_python/minDiamond/runDiamond.cpp
index f5a5395ec..e1ecde5ce 100644
--- a/test_problems/min_python/minDiamond/runDiamond.cpp
+++ b/test_problems/min_python/minDiamond/runDiamond.cpp
@@ -27,8 +27,8 @@ int iDebug_HKM = 0;
 /*****************************************************************/
 /*****************************************************************/
 
-#include "Cantera.h"
-#include "kinetics.h"
+#include "cantera/Cantera.h"
+#include "cantera/kinetics.h"
 
 using namespace Cantera;
 
diff --git a/test_problems/min_python/negATest/negATest.cpp b/test_problems/min_python/negATest/negATest.cpp
index 9d186bfbb..a1f5bde9d 100644
--- a/test_problems/min_python/negATest/negATest.cpp
+++ b/test_problems/min_python/negATest/negATest.cpp
@@ -1,14 +1,14 @@
 
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "ctml.h"
-#include "GasKinetics.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/ctml.h"
+#include "cantera/kinetics/GasKinetics.h"
 #include "importCTML.h"
-#include "ThermoPhase.h"
-#include "InterfaceKinetics.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/kinetics/InterfaceKinetics.h"
 #else
-#include "Cantera.h"
-#include "kinetics.h"
+#include "cantera/Cantera.h"
+#include "cantera/kinetics.h"
 #endif
 
 using namespace Cantera;
diff --git a/test_problems/mixGasTransport/mixGasTransport.cpp b/test_problems/mixGasTransport/mixGasTransport.cpp
index 6fd70b867..ce02ada50 100644
--- a/test_problems/mixGasTransport/mixGasTransport.cpp
+++ b/test_problems/mixGasTransport/mixGasTransport.cpp
@@ -32,11 +32,11 @@ using namespace std;
 /*****************************************************************/
 /*****************************************************************/
 
-#include "Cantera.h"
-#include "transport.h"
-#include "IdealGasMix.h"
+#include "cantera/Cantera.h"
+#include "cantera/transport.h"
+#include "cantera/IdealGasMix.h"
 
-#include "kernel/TransportFactory.h"
+#include "cantera/transport/TransportFactory.h"
 
 using namespace Cantera;
 
diff --git a/test_problems/multiGasTransport/multiGasTransport.cpp b/test_problems/multiGasTransport/multiGasTransport.cpp
index ab665bdfc..ceac0e7ca 100644
--- a/test_problems/multiGasTransport/multiGasTransport.cpp
+++ b/test_problems/multiGasTransport/multiGasTransport.cpp
@@ -32,11 +32,11 @@ using namespace std;
 /*****************************************************************/
 /*****************************************************************/
 
-#include "Cantera.h"
-#include "transport.h"
-#include "IdealGasMix.h"
+#include "cantera/Cantera.h"
+#include "cantera/transport.h"
+#include "cantera/IdealGasMix.h"
 
-#include "kernel/TransportFactory.h"
+#include "cantera/transport/TransportFactory.h"
 
 using namespace Cantera;
 
diff --git a/test_problems/negATest/negATest.cpp b/test_problems/negATest/negATest.cpp
index 2f133b834..7dd7a9fed 100644
--- a/test_problems/negATest/negATest.cpp
+++ b/test_problems/negATest/negATest.cpp
@@ -1,5 +1,5 @@
-#include "Cantera.h"
-#include "kinetics.h"
+#include "cantera/Cantera.h"
+#include "cantera/kinetics.h"
 
 #include <string>
 
diff --git a/test_problems/printUtilUnitTest/pUtest.cpp b/test_problems/printUtilUnitTest/pUtest.cpp
index 3e5c55138..cc243c6df 100644
--- a/test_problems/printUtilUnitTest/pUtest.cpp
+++ b/test_problems/printUtilUnitTest/pUtest.cpp
@@ -3,9 +3,9 @@
 #include <cmath>
 #include <sstream>
 
-#include "Cantera.h"
-#include "kernel/PrintCtrl.h"
-#include "kernel/LogPrintCtrl.h"
+#include "cantera/Cantera.h"
+#include "cantera/base/PrintCtrl.h"
+#include "base/LogPrintCtrl.h"
 
 using namespace Cantera;
 using namespace std;
diff --git a/test_problems/pureFluidTest/testPureWater.cpp b/test_problems/pureFluidTest/testPureWater.cpp
index a6542bcde..07285ac32 100644
--- a/test_problems/pureFluidTest/testPureWater.cpp
+++ b/test_problems/pureFluidTest/testPureWater.cpp
@@ -1,4 +1,4 @@
-#include "PureFluid.h"
+#include "cantera/PureFluid.h"
 #include <new>
 #include <cstdio>
 #include <cmath>
diff --git a/test_problems/silane_equil/silane_equil.cpp b/test_problems/silane_equil/silane_equil.cpp
index f2200ce6c..eef095ba8 100644
--- a/test_problems/silane_equil/silane_equil.cpp
+++ b/test_problems/silane_equil/silane_equil.cpp
@@ -3,14 +3,14 @@
  */
 
 #ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "ThermoPhase.h"
-#include "IdealGasMix.h"
-#include "equil.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equil/equil.h"
 #else
-#include "Cantera.h"
-#include "IdealGasMix.h"
-#include "equilibrium.h"
+#include "cantera/Cantera.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/equilibrium.h"
 #endif
 
 using namespace std;
diff --git a/test_problems/spectroscopy/spectratest.cpp b/test_problems/spectroscopy/spectratest.cpp
index c5dacd16b..e394c6a8b 100644
--- a/test_problems/spectroscopy/spectratest.cpp
+++ b/test_problems/spectroscopy/spectratest.cpp
@@ -1,7 +1,7 @@
 
-#include "Cantera.h"
-#include "spectra.h"
-#include "kernel/Nuclei.h"
+#include "cantera/Cantera.h"
+#include "cantera/spectra.h"
+#include "spectra/Nuclei.h"
 #include <iostream>
 using namespace std;
 using namespace Cantera;
diff --git a/test_problems/surfSolverTest/surfaceSolver.cpp b/test_problems/surfSolverTest/surfaceSolver.cpp
index 715c4252c..64eb89332 100644
--- a/test_problems/surfSolverTest/surfaceSolver.cpp
+++ b/test_problems/surfSolverTest/surfaceSolver.cpp
@@ -34,12 +34,12 @@ static void printUsage()
 
 }
 
-#include "Cantera.h"
-#include "Interface.h"
+#include "cantera/Cantera.h"
+#include "cantera/Interface.h"
 
-#include "kinetics.h"
-#include "kernel/ImplicitSurfChem.h"
-#include "kernel/solveSP.h"
+#include "cantera/kinetics.h"
+#include "kinetics/ImplicitSurfChem.h"
+#include "kinetics/solveSP.h"
 
 using namespace Cantera;
 
diff --git a/test_problems/surfSolverTest/surfaceSolver2.cpp b/test_problems/surfSolverTest/surfaceSolver2.cpp
index 79ebd17b8..54232ac47 100644
--- a/test_problems/surfSolverTest/surfaceSolver2.cpp
+++ b/test_problems/surfSolverTest/surfaceSolver2.cpp
@@ -33,12 +33,12 @@ static void printUsage()
 
 }
 
-#include "Cantera.h"
-#include "Interface.h"
+#include "cantera/Cantera.h"
+#include "cantera/Interface.h"
 
-#include "kinetics.h"
-#include "kernel/ImplicitSurfChem.h"
-#include "kernel/solveSP.h"
+#include "cantera/kinetics.h"
+#include "kinetics/ImplicitSurfChem.h"
+#include "kinetics/solveSP.h"
 
 using namespace Cantera;
 
diff --git a/test_problems/surfkin/surfdemo.cpp b/test_problems/surfkin/surfdemo.cpp
index 0f8169643..452c7e069 100644
--- a/test_problems/surfkin/surfdemo.cpp
+++ b/test_problems/surfkin/surfdemo.cpp
@@ -2,11 +2,11 @@
  *  Sample program that solves an implicit problem for surface
  *  site fractions.
  */
-#include "Cantera.h"
+#include "cantera/Cantera.h"
 #include <iostream>
 
-#include "IdealGasMix.h"
-#include "Interface.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/Interface.h"
 
 using namespace Cantera;
 using namespace std;